AChE bivalent inhibitors (Part II)

This page is a continuation of the page AChE bivalent inhibitors
 * 1w4l TcAChE complex with bis-acting galanthamine derivative
 * 1u65 TcAChE complex with anticancer prodrug CPT-11
 * 1e3q TcAChE complex with BW284C51
 * 1acl TcAChE complex with decamethonium
 * 1eve TcAChE complex with Aricept
 * 1jjb TcAChE complex with PEG-SH-350



Galantamine derivative (compound 3)
Described in the page 'AChE inhibitors and substrates (Part II)' galanthamine (GAL ; colored red ) is an AChE inhibitor and it is currently used in therapy of the Alzheimer's disease (AD). Conjugate of GAL through the alkyl linker (8 carbons, yellow ) with a phthalimido moiety (blueviolet) called compound 3 has a larger affinity for AChE than that of GAL alone. This is similar to previously described cases of bivalent ligands. A comparison between compound 3 /TcAChE (1w4l) and galanthamine/TcAChE structure (1dx6) shows an identical binding mode of the GAL-moiety (transparent red) of compound 3 to that of GAL alone (blue) at the CAS. A PEG molecule (gray) is located at the active site of the galanthamine/TcAChE structure. The alkyl linker spans the active-site gorge and the phthalimido moiety of compound 3 is situated near Trp279 at the PAS. Compound 3 has higher affinity to TcAChE than GAL. This can be explained by the higher number of interactions between compound 3 (which interacts not only with residues within CAS but also within PAS) and TcAChE relative to GAL.

CPT-11
The drug CPT-11 (yellow) interacts with 13 residues of the active-site gorge from Trp84 at the bottom to Phe284 at the top (1u65). Nine of these residues are aromatic <font color='darkmagenta'>(Tyr70, Trp84, Tyr121, Trp279, Phe284, Phe330, Phe331, Tyr334, and His440; colored dark magenta). The contacts made by the drug at the bottom of the gorge involves <scene name='1u65/Binding_site/6'>complementary surface contacts with Trp84, Tyr121, Phe331, and His440 and, especially, a stacking interaction with Phe330. The carbamate moiety of CPT-11 is seen near residues <scene name='1u65/Binding_site/4'>Phe331 and Tyr334. <font color='magenta'>Carbon C9 (shown in magenta) of the carbamate linkage in CPT-11, is 9.3 Å from <scene name='1u65/Binding_site/5'>Ser200 <font color='red'>Oγ, the nucleophilic atom  within the three catalytic residues Ser200, His440, and Glu327. The steric clashes between CPT-11 and TcAChE residues bar the positioning of CPT-11 near Ser200 Oγ (where hydrolysis could occur), therefore, TcAChE can not hydrolyze CPT-11.

BW284C51
In a similar fashion to other AChE bivalent inhibitors, <font color='magenta'>BW284C51 (BW) binds to TcAChE (1e3q) at both subsites of its <scene name='1e3q/Active_site/1'>active site - CAS and PAS. At the CAS, the BW makes a cation-aromatic interaction via its quaternary group to <scene name='1e3q/Active_site/2'>Trp84 <font color='orange'>(colored orange). The BW phenyl ring forms an aromatic-aromatic interaction with His440. There is also an electrostatic interaction between the BW proximal quaternary group and Glu199. Near the PAS, BW via its distal quaternary group, interacts with <scene name='1e3q/Active_site/3'>Trp279 <font color='cyan'>(colored cyan) and forms an aromatic interaction with Tyr334. BW forms hydrogen bond with Tyr121 OH, and makes alkyl interactions with Phe331. The superposition of BW with two other AChE bivalent inhibitors <scene name='1e3q/Active_site/4'>DECA <font color='gray'>(decamethonium, colored gray, 1acl) and <scene name='1e3q/Active_site/5'>E2020 <font color='blueviolet'>(Aricept, colored blueviolet, 1eve) at the TcAChE active site gorge reveals similar mode of binding. These 3 inhibitors form cation-π and π-π interactions with active-site gorge aromatic residues <scene name='1e3q/Active_site/6'>(Tyr70, Trp84, Trp279 and Phe330 or Tyr334) <font color='black'>(colored yellow). The superposition of <scene name='1e3q/Active_site/7'>DECA and E2020 reveals their similar trajectory along the active site gorge, but <scene name='1e3q/Active_site/8'>BW has a different one. This results in <scene name='1e3q/Active_site/9'>different conformation of Phe330, which interacts with BW more strongly  than with DECA and E2020. The conformations of the other important residues at the active site are similar in all these inhibitor complexes. It has been shown experimentally that BW and E2020 bind to TcAChE approximately 100-fold stronger than DECA. These findings have several explanations: i) E2020 and BW are less flexible than DECA; ii) the aromatic groups of E2020 and BW form favourable π-π interactions with TcAChE aromatic residues, in contrast to DECA; and iii) <scene name='1e3q/Shape/3'>BW and <scene name='1e3q/Shape/2'>E2020 have aromatic groups and, therefore, occupy more volume and better fit the active-site gorge, than <scene name='1e3q/Shape/4'>string-shaped DECA . Mutations at the mouse or chicken AChE residues, corresponding to the TcAChE <scene name='1e3q/Active_site/10'>Tyr70, Trp84, Trp279 and Tyr121 <font color='red'>(colored red), cause significant increase of inhibition constant values for all these 3 inhibitors, supporting the notion that these residues are critical for inhibitor-AChE binding.

PEG-SH-350
<scene name='1jjb/Active_site/1'>PEG-SH-350 is an untypical acetylcholinesterase inhibitor (1jjb). It consists of heptameric polyethylene glycol (PEG) with a thiol group (SH) at the terminus. The thiol group binds close to the <scene name='1jjb/Active_site/4'>catalytic anionic site (CAS) and the second terminus binds to the <scene name='1jjb/Active_site/5'>peripheral anionic site (PAS). PEG-SH-350 interacts with Torpedo californica acetylcholinesterase via a system of <scene name='1jjb/Active_site/6'>water molecules <font color='red'>(represented by oxygens colored red). Two out of the seven PEG-SH-350 ethylene glycol units are in trans <scene name='1jjb/Active_site/7'>conformation <font color='blue'>(colored blue), while the others are in ±gauche <scene name='1jjb/Active_site/8'>conformation.

Aricept
Aricept. Among the most interesting drugs that have been designed to inhibit acetylcholinesterase are those that have two binding sites that bind both the peripheral and catatylic sites simultaneously. Such drugs bind strongly and with high specificly. A good example is <scene name='Acetylcholinesterase/1eve_e2020/1'>the E2020/TcAChE (Aricept) complex (1eve). It appears that the principal interaction between the aceylcholine and the enzyme is the relatively newly discovered cation-pi interaction between the cationic moiety of the substrate and the many aromatic residues lining the catalytic gorge. Unlike most interatomic interactions in chemistry, cation-pi interactions are unusual in that their energy hardly changes as the cationic and aromatic ring centers distance vary between 4 and 7 Å, and for a wide variety of relative orientations of the aromatic rings. This gives the substrate an energetically smooth ride down the gorge with few bumps or barriers to impede passage down the gorge. Most acetylcholinesterases have a net negative charge and a large patch of negative potential around the entrance to the active site gorge. This may be useful to attract the positively charged acetycholine substrate to the site. As one travels down the gorge, this potential becomes increasingly more and more negative, reaching a peak at the active site at the base. Because of this potential, the peripherial site is thought to act like a substrate trap, that forces practically every molecule of substrate that reaches the peripheral site to travel down the gorge to the active site. This probably contributes greatly to the extremely rapid rate of degrading the substrate. This whole enzyme therefore acts like a brilliantly designed natural vacuum cleaner that clears the neurotransmitter out of the synapse extremely quickly. Yet to be solved, however, is how the products clear the active site rapidly, whether back through the gorge, or out a back door on the other side of the protein that quickly opens each catalytic cycle (Trp84 is actually near the surface at the 'underside' of the protein). The X-ray structure of the E2020-TcAChE complex shows that E2020 has a <scene name='1eve/E2020_close_up_with_84_279/13'>unique orientation along the active-site gorge, extending from the anionic subsite (<scene name='1eve/E2020_close_up_with_84lbld/7'>W84 ) of the active site, at the bottom, to the peripheral anionic site (<scene name='1eve/E2020_close_up_with_84_279lbld/5'>near W279 ), at the top, via aromatic stacking interactions with conserved aromatic acid residues. E2020 does not, however, interact directly with either the catalytic triad or the 'oxyanion hole' but only <scene name='1eve/E20_interactionshown/8'>indirectly via solvent molecules.

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Additional Resources
For additional information, see: Alzheimer's Disease